Gene Expression
Nebulas
Gene Expression NebulasSummary: We conducted a genome-wide transcriptomic analysis in soybean leaves treated with a short-term (24 h) Pi-deficiency using RNA sequencing (RNA-seq) technology. Two biological replicates of RNA-seq were included for both Pi-sufficient leaves (PSL) and Pi-deficient leaves (PDL), and therefore a total of four libraries were constructed. Using a 2-fold change and a P-value ≤0.05 as the cut-off for selecting the differentially expressed transcripts, we globally identified short-term Pi-stress responsive genes. Some DEGs potentially involved in Pi sensing, signaling, and homeostasis were up-regulated by Pi deprivation, including five SPX-containing genes. Some DEGs possibly associated with water and nutrient uptake, hormonal and calcium signaling, protein phosphorylation and dephosphorylation, and cell wall modification were affected at the early stage of Pi deprivation. At least thirty-one transcription factor genes belonging to 10 diverse families were found to be responsive to Pi starvation.
Overall Design: The first trifoliate true leaves of soybean were harvested after 24 h treatment with or without phosphate, and RNA was extracted and sequenced by paired-end sequencing. RNA sequencing reads were aligned against the soybean reference genome and differentially expressed genes between treatments were detected.
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| Growth Protocol: | Soybean (Glycine max var. Williams 82) seeds were soaked in sterilized water for 4 hours, and then incubated at room temperature in the dark between two layers of moistened filter paper. Four days later, seedlings were grown hydroponically in a 10 L tank filled with half-strength modified Hoagland nutrient solution containing 2.5 mM Ca(NO3)2, 2.5 mM KNO3, 0.5 mM KH2PO4, 1.25 mM MgSO4, 10.0 μM Fe-EDTA, 3.4 μM MnSO4, 0.16 μM CuSO4, 0.38 μM ZnSO4, 23.0 μM H3BO3, 0.25 μM Na2MoO4, with pH adjusted to 5.6. Nutrient solution was changed every two days. Plants were grown in a growth chamber with a photoperiod set at 16-h-light/8-h-dark at 26/22 ◦C and light intensity set at 150 μmol m-2 s-1. |
| Treatment Protocol: | After 18 days of cultivation, soybean seedlings with the first trifoliate true leaves fully expanded were transferred into Pi-sufficient (500 μM KH2PO4) or Pi-deficient (0 μM KH2PO4, K2SO4 was substituted for KH2PO4) nutrient solutions. |
| Extract Protocol: | Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s procedure. |
| Library Construction Protocol: | RNA libraries were prepared for sequencing using standard Illumina protocols |
| Molecule Type: | poly(A)+ RNA |
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| Library Layout: | PAIRED |
| Library Strand: | Reverse |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina HiSeq 2000 |
| Strand-Specific: | Specific |
| Data Resource | GEN Sample ID | GEN Dataset ID | Project ID | BioProject ID | Sample ID | Sample Name | BioSample ID | Sample Accession | Experiment Accession | Release Date | Submission Date | Update Date | Species | Race | Ethnicity | Age | Age Unit | Gender | Source Name | Tissue | Cell Type | Cell Subtype | Cell Line | Disease | Disease State | Development Stage | Mutation | Phenotype | Case Detail | Control Detail | Growth Protocol | Treatment Protocol | Extract Protocol | Library Construction Protocol | Molecule Type | Library Layout | Strand-Specific | Library Strand | Spike-In | Strategy | Platform | Instrument Model | Cell Number | Reads Number | Gbases | AvgSpotLen1 | AvgSpotLen2 | Uniq Mapping Rate | Multiple Mapping Rate | Coverage Rate |
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